Pokemon Adventures
by TheFlyingEyeball
Summary: Follow Green, an orphan from Kanto, as he enters a Pokemon Academy in Kalos where he learns the values of friendship, love, and more. Current ships include Oldrival, Knowledge (Crystal x Gary), Power (Tobias x Zinnia), Ikari, Frantic, Special.
1. 10 years ago

Green returned home from his adventure in Kanto. After a long and cruel year and a half, he finally did it. He became the champion! But what now? He had no friends, no family, other than his cousin who he hasn't seen in forever, and most importantly, he had no home. His house was burned down when he was just 5 years old. It was a miracle he survived.

Contemplating on what to do next, he heard a voice go through his head, _Head to Victory Road. I'll wait for you there._

Taking this as a call to adventure, he flew back to Victory road and sure enough, someone was waiting for him. The man was in a hooded emerald-velvet cloak, so he couldn't see his face. The stranger held out his hand to Green, and Green took it.

The two were warped away, and ended up on a secluded island.

Removing his hood, the figure spoke. "My name is Emerald, one of the seven Pokemon Master-Elites. Your training begins tomorrow, so get some rest."

Master-Elites? The people only talked about in legends? Green could not believe it. He clenched his fists, he was ready for anything.


	2. Present

It has been 10 years since he first left to train, and 5 years to finish it. Green spent the next 5 years after that traveling to different regions a changed man. He was no longer a child, he was the graduated student of a Master-Elite. But this did not distract him from getting stronger. He was now very secluded, only acknowledging very few people. He was known through nearly every region for his overwhelming strength from little effort showing. Yes, Green may have changed, for better and worse, but some things about him never changed, including his thirst for adventure and the thrill of fighting powerful trainers, though the second one has been lacking for quite some time.

He was journeying back to Kalos to enter a special academy which his master said is where his destiny lies. He reached the school and a woman called Cynthia was there to meet him.

"Long time no see Green! How are you doing?" Asked Cynthia?

Green said nothing, but nodded to acknowledge her.

"I swear, every time I see you, you change more and more" Cynthia said. Green just shrugged. "Anyways, welcome to the Crimson Academy! Here, trainers, breeders, and coordinators learn under the best! Since you are registered as a trainer, Lance and Mars should be here soon. Here, trainers are split into three groups, Class A, Class B, and Class C. If you beat Mars, you're in Class B, then you have the eligibility to get to Class A by then beating Lance!"

Green began to wonder why Emerald would want him to come here. But he stopped thinking about it. It was unwise to question a Master-Elite. Emerald knew what he was doing.

At this point, Lance and Mars showed up. "Hello again Green." said Lance.

"Remember me?" asked Mars. Mars used to be an admin for Team Galactic, but once it disbanded, the three admins were released from prison and all recieved jobs as teachers at the Academy"

"Let's go to the battle room and get this going" they both said. Green followed.


	3. Chapter 1 New Member

A person wearing red clothing and a red hat was running towards a group of people. "Blue, Tobias, Yellow, Gold! There's a new student! He is battling Lance right now! Hopefully we can see some of it before Lance crushes him!"

The 5 people sprinted to the battle room, but it was too late. The match was over.

"Damn!' said Gold. "Looks like Lance had no trouble here!"

Cynthia walked to the center of the room and announced, "It's official! Green has beaten Lance in extraordinary time! He is in Class A"

"WHAT?" cried the group. "This guy beat Lance that fast?"

Cynthia turned towards them and spoke. "Ah Red! I was about to call you. I'm leaving you in charge of showing Green around the academy. Moreover, he's your new roommate!"

"Whatever" he thought. "This kid can't possibly beat me!"


	4. Chapter 2 New Roommate

Red showed Green around the campus. It was still a week before classes began, but everyone from Class A was present. After 2 hours, the tour was over. Red looked at Green and said "It is tradition for Class A to hold a giant tournament to rank everyone. Class B does it as well, but at a different location. Our's is more exciting though. We begin tomorrow, so get ready for that. Anyways, here is our room, you can put your stuff on the left side. Sorry about the mess, I wasn't expecting a roommate."

Green just shrugged and dropped his stuff on the left side of the room. Quickly he unzipped his bag and pulled out many things, including a picture frame with a burnt photo inside and a giant book. Red said nothing. It was late, and the tournament begins tomorrow. He felt bad for Crystal and White. The two girls now have to fix the tournament matchup sheets.

Next day came and Red awoke to his roommate's bed empty. Looking out the window, he saw Green meditating next to an Alakazam. Even from that far away, Red felt a psychic power coming from that pokemon that was strong enough to rival Mewtwo's.

 _Just who is this guy?_ Red thought. But he had no time to waste, the tournament begins in 2 hours. Red looked back to Green to call him, but he was gone.

Red walked down to the Mess Hall and sat down with his usual group of friends: Gold, Yellow, Tobias, and Blue. Red looked around and soon saw Green eating alone. He thought about sitting with him, but something in his head told him that Green would rather be alone.


	5. Chapter 3 Tradition

All of Class A entered the Battle room, and Crystal explained the matchups. "Ok! So we have Red going against Black, Blue against White, Gold against Sapphire, X vs Sun, Me vs Y, Silver vs Diamond, Pearl vs Green, Platinum vs Yellow, and Tobias vs Moon. Ok! Is everyone ready? First round, Start!"

Green watched in boredom as the Class A battled. So far, the only ones to remotely interest him was Red and Tobias. Red easily blew through Black and moved on. Other winners were Blue, Gold, X, Crystal, Silver, Tobias, and Yellow. Finally, Green was up. The battle was over in less than 10 minutes. Green's Charizard one-shot all of Pearl's pokemon. Many of the other Class A members were stunned.

Crystal was the first to speak. "Jesus! *Ahem* Anyways, that concludes round one! We will take a lunch break and begin Round 2 after.

Again, Green sat alone, when suddenly Pear shot towards him and began to accuse him of cheating. "YOU HAD TO BE!" He cried. "NO ONE IS THAT STRONG! HOW CAN ANYO-" He was cut short when Green gave him a cold glare.

After that incident, Round 2 began. Crystal spoke. "Ok, in this round, we have Blue vs Me, X vs Green, Gold vs Tobias, and Silver vs Yellow. Red, take a break. You were the best last year, so you're done until the final round." And with that round two started.

Blue and Crystal went at each other. Their pokemon slowly going down from each attack. And in the end of this struggle, Blue edged out. Tobias shot through Gold without breaking a sweat. Green was mildly interested by his Darkrai. Silver was just beneath Yellow in their match. Once again, Green obliterated X almost immediately. With that, the day was over.

That night, Red looked intimidated by Green. _Just how powerful is he? His Charizard's energy is nothing like I've ever seen before!_


	6. Chapter 4 Green vs Red

The next day marked the beginning of the final day of the tournament. At breakfast, Blue tried to chat with Green. "So it looks like I'm against you first. I know you're stronger than me, but I'll still give it my all!" As she was leaving, she could have sworn she heard Green reply "Glad to hear."

In the next round, Tobias shot through Yellow, and Green blew through Blue.

When Green finally battled Tobias, both were curious to see what the other had planned. The battle took around 30 minutes, and Green was victorious. Everyone was stunned. Green's Charizard blew through everyone while only taking minor damage. Green was slightly impressed with Tobias's team, but still disappointed about the match. He had gotten his hopes up for nothing. With that, Red stepped up and the final round was on!

After a cruel match (from Red's POV), Red was down to one pokemon, while Green still had all 6. Then, Red had an idea. He yelled some different language and within a minute, Mewtwo appeared before him.

 _It will be an honor to fight for you Red!_ He said, and the final battle continued. But something was different. Green, who was on the attack during every match before, was only ordering his pokemon to dodge. This made Red angry. "STOP HOLDING BACK!" he yelled. "SHOW ME YOUR TRUE STRENGTH!"

Everyone looked at Green who was now smiling. "Fine. If you want this to end so badly, so be it". And with that, white energy began to shoot off of Green and land on Charizard. Mega Evolution. Charizard was now black and much bigger. Mewtwo didn't even see it coming. One moment Mega Charizard X was staring right at Mewtwo, when all of a sudden, Mewtwo was knocked out. Charizard didn't even seem to move. The tournament was over. Green had won.

Green began to speak. "When I first saw you and Tobias battle yesterday, I was actually interested. Looks like it was for nothing. I still didn't use my full strength." And with that, he walked off. It was 9:00. Dinner time.


	7. Chapter 5 The Past

Green was eating alone again, when suddenly, Red's group sat down next to him. He was immediately filled with questions. "How are you so strong? Can you train me? Just who are you?"

Green sighed. "My name is Green Stone. I am from Kanto. After winning the league, I trained for 5 years before setting out again"

"Where?!" they all asked, but Green didn't answer. He just finished eating and went to his room. Red joined in later.

"Hey, we are all going to the Rec room tonight to watch a movie, you should come. It'll give you a chance to open up" said Red. Green just shrugged. Green did not go with them. He stayed behind to read the large history book he packed. He continued reading all through the night, only finally falling asleep at 4:00 in the morning.

The next day was the same as before, people pestering Green about his strength, asking how and where he did it. Again, Green said nothing. Around noon, Blue knocked on his room door.

"Hey, do you mind if I stay a bit? All the boys are playing cards and the girls are talking about god knows what. I'd hang out with Yellow, but she's at the Safari Zone with Red".

Green just shrugged and Blue entered. "I don't think I've ever introduced myself." explained Blue. "My name is Blue Leafgreen. I'm from Kanto, just like Red, Yellow, and you." Green nodded. Then Blue noticed the burnt photo. "If you don't mind me asking, who are the people in that photo?" Green said nothing, but a single tear could be noticed running down his face. Then, Blue understood who they were.

"I lost my parents too." she began. "I don't remember it completely though. I was very young, but remember it clear enough. They both died from disease. Cancer, if I remember correctly." She paused for a moment. "What about you?"

Green said nothing, so Blue decided to leave him alone. However, just when she was about to open the door, Green spoke.

"There was a fire."

Blue turned around. "Excuse me?"

"I was 5 at the time, yet the memory was burned into my head. A fire. Started out with a gas leak. Then my mother turned on the stove and the house went up in flames. Oak managed to get me out in time, but my parents couldn't be saved. They burned alive in there." At this point, Green was crying. He remembered everything. He felt guilty for taking his family, his home, for granted. "Since then, I never had any human friends".

Blue sat down next to him. Listen, all of us are trying to be your friends. Why won't you let us help?"

Green only replied in a whisper. "So I'm not the cause of more pain". Blue both shocked and confused. He didn't say that is sadness, but rather, it sounded like grief and anger. But why?

"You don't have to worry about us" Blue replied. "We're the best of the best!"

Green looked up. "Alright. I'm trusting you all."


	8. Chapter 6 A Week Later

The whole campus was now filled with trainers of all Classes. Green also noticed groups of breeders, as well as coordinators. He soon found his friend group and joined them. Over the past week, Green had started to loosen up with the Class A members, and had made good friends with Red's group. He found Red and someone else messing with a small kid with a Pikachu on his shoulder.

Green sighed. Gary and Ash. When will those two stop? He knew Gary quite well growing up and learned about Ash from him, and from what Gary described, he still acted like a child. Green saw that this was true.

Red was the first to notice Green. "Hey Green, come over here! There's some people I'd like you to meet!" Green walked over. "This over here is Ga-" Green interupted him.

"Hello there Gary. How goes your studies in Sinnoh?" asked Green.

"Well well well! Seems you finally relaxed!" noted Gary. "Things have been going well."

Red chimed in. "You two know each other already? Great! Saves me the trouble. Well then, over here is Ash. He's the 3rd or 4th best member of Class B, but still acts like a little kid."

"I DO NOT!" yelled Ash. Green looked at him. He didn't look or act different from some of the other Class B trainers, but then again, looks can be deceiving.

Green's thoughts were interrupted by the sound of a large, ringing bell. "Looks like it's 8:20. Ten minutes before our first class. Come on Green. Let's not be late" Red spoke. And with that, the two left for their first class.


	9. Chapter 7 The Message

The first day was pretty boring. Astronomy, Advanced Battle Techniques, EV trainings, and Nature Studies. None interested Green. He finally received his break at lunch. Sitting next to Red and Blue, as they told stories about how interesting ABT was and so forth. But Green's mind was elsewhere. Why did Emerald want him to come here? Should he really be so close to others? And more importantly, what's with that sudden headache? _Headache?_ Green thought, _That's weird, it just came out of nowhere._ Then he suddenly passed out.

Green awoke back in Pallet Town. He looked around, he was in his home. But that was impossible. His home was burnt down. Suddenly, four shadow figures barged into the house. His parents fought with everything they had, but were quickly dealt with and now laid dead on the floor. Green heard one of them speak, "Sir! What shall we do with the toddler?" Another replied, "Leave him. Burn the house. If he survives, who cares? Our mission was to kill the Student of Emerald!"

The men then proceeded to burn everything. Green tried to attack them, but his fists fased right through them. Green collapsed. Why? Why was he living through this again? Suddenly, the whole world went grey, except for one of the shadowed figures. He turned around and faced Green, as if knowing he was there. "I know you're confused and scared, and above all else, enraged. We finally tracked you down, after all these years. If you don't want any harm to come to your new friends, you will meet us in the cemetery, 3 miles west from your academy. Be there at midnight tonight and we shall talk. Don't show up, a friend of yours dies. See you soon, Son of Lunick."

Green woke up sweating. He looked around, he was in the Hospital Room. In front of him were Red, Blue, and Yellow. Blue was the first to speak.

"Oh thank god you're finally awake. You had us worried sick. What happened? Are you ok?"

Green ignored her. He looked at the time. 10:45 pm. Green shot up and sprinted to his room. There, he grabbed a few things. His bag, his 5 other pokeballs (he kept Charizard with him at all times), and a flashlight. He was just about to leave when Red stopped him.

"Now hold on there. You're not going anywhere until you explain what happened."

Green answered, "Please Red, we'll discuss this later, hopefully. I really need to go!

"Just tell me no-" but it was too late, Green was gone.


	10. Chapter 8 The Empire

Green reached the cemetery with 5 minutes to spare. To his left, were 8 shadowed figures. Those were them. Green walked over to them, doing his best to keep his cool. The middle figure spoke. Green concluded him to be this group's commander. "Look who showed up! Long time no see kid."

Green said nothing. The man continued, "Let's cut to the chance. You know where Emerald is. Tell us, and no one gets hurt. Do we have a deal?"

Green answered in a cold tone. "You must think I'm an idiot. I'll never tell you where he is. Besides, you need a key to find the place. So give up. We have nothing to discuss."

The man laughed. "Please. We have the key. We're not leaving until you tell us where he is. And if you do, she doesn't get hurt." They brought in another person with a sack over her head. When they took it off, Green almost went mad. They kidnapped Blue!

"Green?" cried Blue "What's going on? Who are these people? Who's this Emerald guy?"

Green was pissed. He yelled at the commander. "WE MADE A DEAL! WHAT THE HELL?"

"That doesn't matter. Tell us the location and she lives, or don't and she dies. Your choice."

It was at this point Green came up with a plan. It was extremely risky, if it failed, both of them would be killed, along with everyone else at the academy. Tick secretly crawled out of his pocket and scurried over to the men. Tick was a Joltick who was a runt, making him no larger than a Nugget, but his electric attacks were off the charts. Now all Green needed to do was stall them to give Tick enough time to get ready.

"Please, before I say anything, I deserve some answers." Started Green. "Who are you people? And what do you want with Emerald?"

The middle man responded. "Very well. My name is Mazon. I am one of 21 field commanders for the Shadow Empire. Our goal is to bring the eighth fallen Master-Elite back to power. Over the years, we have erased 3 out of the 7 Masters. When all 7 are gone, Vaxil, the 8th Master, will rule. There, we answered you, now answer us! Where is Emerald?"

Everything was ready. Green just needed to give the signal. He laughed. "You know, I've learned that negotiations never work. We make a deal, you break your promise, so I retaliate."

"What do you mean?"

Green just smiled. "Bye."

At that moment, Tick delivered 975 volts of electricity to all 8 men at once. They didn't have time to scream. In an instant, they were lying dead. Their organs burned. Green rushed over to Blue and quickly untied her.

"Blue! Are you ok? Did they do anything to you? What happened? Are the others ok?"

Blue looked at him. "I was captured following you. Thanks for saving me. As far as I know, the others are still at the academy." Then she got serious. "You have some explaining to do."

"Tomorrow, I'll gather all of Class A and explain. As for tonight, stay alert. More can come."


	11. Chapter 9 The Explanation

The next day, Green and Red gathered all of Class A to the Class A rec room. When everyone was accounted for, Green began. "Last night, Blue and I had a run in with a group known as the Shadow Empire. I managed to deal with the group, but now we… no, the whole academy is at risk. If anyone seems suspicious, or goes missing, you report it to either me, Red, Yellow, or Blue. Any questions?"

X spoke up. "A lot actually, but most importantly, who the hell is the Shadow Empire?"

"The Shadow Empire is nothing like any evil corporation any of us has ever faced. They are much more cruel, cunning, sly, and overall beyond evil. They are also much more dangerous and stronger."

Moon spoke next. "What do they want?"

Green explained. "To help a Master-Elite rise over the others."

"What's a Master-Elite?" asked Tobias?

Crystal began to speak. "It's an old legend. For years, trainers fought against each other to be the best. 8 people rose to the very top, becoming the strongest, but beneath the Master God, but since they were so evenly matched, they went their separate ways and began to accept students, but the agreed rules they came up with allowed only one per Master. These Masters had the strength to rival even the Elite God. They can permanently stop their aging, which is how they lived for so long. Nearly a century after the Elites first came to be however, one of the Elite's ambition grew too great, and wanted to rule over everything. This sparked a war between the Masters. However, the 8th was outnumbered 7:1 and fell. But he didn't actually die, many believe that the other seven. Only a combination of powerful attacks, or a Master can truly kill another Master." She finished. "But it's only a legend. Right?"

Green shook his head, "The Master-Elites are very real. I trained under one. Emerald. But they are disappearing. Emerald is the Shadow Empire's target. He will be the 4th one to fall in the past 50 years if they find him."

Green finished the meeting. "Remember, stick together. Sleep in shifts if you have to. Keep your best 6 pokemon battle-ready at all times. Their grunts equal Tobias in strength, so do not let your guard down… EVER! They'll be after you to attract me, even if they do, they'll still kill you in the end." All of Class A understood, but deep down they were terrified. They would need to train extra hard to even stand a chance. Nearby, someone was listening to everything. When Class A started to leave, the figure bolted.


	12. Chapter 10 Class B

Paul swallowed hard. Had he just heard something not meant for anyone besides Class A? All he came to do was try and challenge Silver for the hell of it, and now he knew something he wasn't supposed to. He rushed back to the Class B rec room to try and relax. Trip was in there already. _On second thought, maybe I'll go see Gary._ Paul thought. _Maybe he can help me_ _ **.**_ So he snuck by Trip, hoping he wouldn't see him, and quickly ran to Garry's room.

Paul barged in and immediately began to speak. "Gary! I need your help. Now!"

"Look, can we do this later, I'm having a problem of my own, but since you're here, maybe you can help me. What does Crystal like to do?"

"According to Silver, exploring ancient temples" answered Paul. "but that's not important. I seriously ne-"

"Thanks for the help Paul! See ya!"

Gary got up and tried to bolt out the door, but Paul quickly grabbed Gary's arm. "Can you please be serious here for a minute? This is extremely important!"

"With that kind of look, I'm actually worried. What's up Paul?"

Paul explained everything. The Shadow Empire, the Master-Elites, everything. Gary contemplated on what he just heard. "If what you are saying is true, then we have a serious problem on our hands. If this 'Empire' can strike fear into Green, then Class A will not be enough." He paused for a moment. "Ok, this is what we are going to do: I'll do my best to get more info out of Green, as well as do research on my own. As for you, get the strongest Class B members and create a training program for them. We have to help our Class A brothers."

"Understood, any ideas on who I should tell?"

Gary thought for a moment. "As much as I hate to admit, Ash is a priority here, His Charizard, Sceptile, and Greninja combined can be useful." Then Gary said, "You know what, enjoy your weekend. I'll text you a list of people to join us on Monday. And with that, Gary left to try and spend the day with Crystal, while Paul decided to check in on his girlfriend, Dawn.


	13. Chapter 11 Recruitment

At around noon on Sunday, Paul received a text from Gary. _Here are the people we need: 1. Ash; 2. Gladion; 3. Wally; 4. Iris; 5. Lucas. Good luck. Trying to get info now._

So the B team had been decided. Along with him and Gary, there are 8 members. Hopefully that'll make some kind of difference. The meeting was held after classes the next day.

"Hey everyone!" yelled Ash. "Looks like Paul asked you guys to come too?"

Gladion nodded. _How could Ash be so calm about this?_ He thought to himself. _This is the first time Paul has been this worried about something. Something is wrong._ Lucas seemed to be able to read his thoughts. "I know Gladion is think the same thing as me Ash. Paul looked extremely worried. This isn't something to take lightly."

At that moment, Paul and Gary walked into the Class B rec room and saw everyone else waiting,

"Good" sighed Gary. "They are all here. Paul, you start."

"The other day I overheard Class A's newest member talking about how he and Blue had a run in with a group that is known as the Shadow Empire. Green managed to defeat an entire group single handedly, but only after setting a surprise trap."

Gary continued from what Paul had said. "What makes this group different from teams such as Rocket and Flare is that the Empire kills whoever they beat. So not only are your lives at risk here, each grunt alone has the strength of Tobias. According to Green, these people are trying to kill the Master-Elites, and they have already killed 3 out of 7 in the last 50 years. We chose you 5 to help Paul and I provide, if any, support to the Class A. For now on, observe your surroundings very carefully and take notice of anything suspicion or if anyone goes missing. Have your best team ready at all times, also please let us verify your teams before doing anything stupid. Ash, talking to you Ash! You are dismissed. Have your team ready for us to check by Lunch tomorrow"

Gary walked up to Ash. You need to be very serious about this. I recommend Pikachu, Goodra, Greninja, Infernape, Charizard, and Krookodile. Have Sceptile, Lycanroc, and Herocross on reserve.

"Don't worry about me!" laughed Ash. "I'll be fine!"

 _Saying that makes me worry_ , thought Gary.

The next day, Green, Red, Paul, and Gary were discussing reinforcement options. Paul decided using Class C all together, but the others agreed that was suicide.

"What if we use the organizations we fought against before as backup?" suggested Gary.

Green perked up. "That's actually a great idea. Tobias and Gary, you go to Hoenn. Convince Aqua and Magma. Red, you and Paul go for Plasma. Silver and I will go to Kanto to get Rocket. Lastly, we'll have all 3 Galactic Admins go to Sinnoh and explain what's going on after I explain the situation to them. Though Galactic is disbanded after Cyrus's disappearance, there's gotta be some members still willing to follow the Admins. Good luck everyone! Stay safe and stick together."


	14. Chapter 12 Old Enemies (Rocket) pt 1

Green and Silver landed in Kanto and began to travel to the old Rocket HQ. Thankfully, Silver managed to get in touch with his father before they left to travel to Kanto. He had to be brief, explaining how he and a friend needed to talk to him immediately. Giovanni, though suspicious about why his son would contact him after so many years, agreed. He said he would send an Executive member along with a team of grunts to escort them from the old HQ. Green kept himself hooded, along with having his Alakazam use his physic abilities to hide his true self, just to be sure. Silver was very impressed with Green's Alakazam. It was emitting that much Psychic power despite still being in its pokeball. They reached the entrance to the old HQ within a week. There, Executive member Proton, as well as several grunts were waiting for them there.

"Ah, Master Silver" exclaimed Proton, "It's so nice to hear from the boss's son again."

Silver looked annoyed. "I gave up on Team Rocket years ago. The only reason we're here is because it's an emergency. Look, we don't have much time, we could've been followed for all we know."

Proton, looking confused, responded in a worry manner. "Oh? What is going on?"

Silver then whispered, "The man next to me is Green. I'm sure you know of him. He'll explain what's happening."

Proton then looked at Green. "You again! If you weren't with the boss's son right now, I'd have everyone attack you! You have some nerve showing up he-"

"Just, shut up!" Green interrupted. "We can argue later. Right now, we need Team Rocket's assistance. We've encountered the Shadow Empire a while back. I know the texts say they died out, but they're wrong. They are still out there. And stronger than ever."

Proton laughed. "Please, the Empire can't attack us. Even if they do, we'll destroy them. So stop worrying"

"The boy is correct to worry!"

Proton, the grunts, Silver, and Green spun around and saw seven Empire members behind them. Silver was right. They were being followed!

"Green, you should've known this was going to happen! I am ashamed" said the commander. "The Empire also sent groups to Hoenn, Sinnoh, and Unova as well. None of your friends are leaving alive!"

He was right. Green knew they would show up again, but it was a risk he had to take! Proton started to speak. "So, what he's saying is true. The Empire remains. Well not for long! Team Rocket! Attack!" Suddenly, around a hundred more grunts bursted out from nearby bushes, trees, and holes. Giovanni had sent backup. Pokemon attacks were everywhere.

Proton grabbed Green and Silver. "Quickly! Inside! Go!"

Proton, Silver, and Green ran inside the HQ and soon found Sabrina waiting there. Sabrina was a gym leader, but also a member for Team Rocket. Her Alakazam used Teleport, and all 4 people were transported to the Team Rocket Airship. They ended up in front of Giovanni.


	15. Chapter 13 Old Enemies pt 2 (Rocket 2)

Giovanni was the first to speak. "Are you all alright? Proton, what happened to all the grunts I sent you?"

Proton took his hat off. The two were followed. By now 112 grunts are lying dead in the grass in front of the old HQ."

Giovanni was shocked! "What? How? Explain!"

Silver spoke. "Dad, listen. Unknowing to my friend here and me, we were followed by a group from the Shadow Empire."

"That's impossible, they were wiped out over a century ago!"

"No. That never happened. The Empire faked their own demise so the regions can break the alliance they made. They attacked us at the old HQ. The surprise attack set up by Proton saved us."

Giovanni looked very concerned. "You" pointing to Green, "who are you, and did you have any cause in this?"

"You know me. The name is Green. They are after me because I know the location to a Master-Elite. You know they are real. You've met my father. You've seen his training. An Empire Field Admin killed him years ago. Now, one of their grunts alone can match the power of our 3rd best trainer at the academy. An entire group is basically unstoppable. I managed to wipe a group out 8 out with a surprise attack. But the fact that it worked was sheer luck."

Giovanni tried to keep his cool. "The Empire was a force to be reckoned with a century ago, and now? If what you are saying is true, then they are more powerful than ever. Team Rocket offers their full support to defeating them. I will contact the other members to tell them the story. Surge will be important. He's the only member with true military experience."

"Thanks father, we also have 3 more groups at Hoenn, Sinnoh, and Unova. I hope they're-"

Green shot in, "Wait, didn't they say they sent groups to attack them?" Oh crap!" Green quickly called up Red, Tobias, and Saturn. "This is Green. Rocket has entered! Is anyone there? Hello? Anyone?"

There was only static. Green went into shock. If the Empire got to them, their chance of survival is basically non-existent. Suddenly, he heard crackling from the phone.

" _This is Saturn. Galactic is non-existent."_

" _This is Red. Plasma is gone."_

" _This is Gary. Magma and Aqua has fallen."_

Red began to speak. " _We are all back at the academy. We managed to get remnants from each team out during the chaos. They are currently healing up as we speak. Get Rocket here ASAP"_.


	16. Chapter 14 Old Enemies pt 3 (Hoenn 1)

3 days before Green and Silver set out to Kanto, Gary and Tobias entered Hoenn and discussed their plan of action. Gary suggested that they should split up. "We would be less noticeable, meaning, less attention will be drawn towards us.."

Tobias disagree. "If we were in any other scenario, that would be smart. However, that move is extremely risky. Is the Empire shows up, we'll be doomed. We stick together. It'll be safer." And with that they began their travel to Lilycove Cave. Luckily, when a Magma grunt tried to challenge them, the two refused, but said that they need to speak to Maxie immediately, and that all of Magma should meet up with Aqua at the cave. Tobias has to use force to get the grunt to comply. And within a few days, they were standing in front of Lilycove Cave. Two Magma and Aqua grunts escorted them inside.

Gary looked around. He saw the two teams constantly bickering at one another. _Hopefully we can make them get along in time,_ thought Gary.

At last, they were face to face with Archie and Maxie, who were accompanied by Admins Matt, Shelly, Tabitha, and Courtney. Each Admin looked like they wanted to tear apart the other team's leader. Archie was the first to speak. "You have some balls to have all of Magma show up to this meeting. All sides are on edge."

Tobias spoke up. "Trust me, none of you know what 'on edge' is"

"Oh really?" Maxie replied. "Please, explain to us why you are on edge!"

Gary shot at both leaders. "Both of you need to grow up! We wouldn't have wanted to meet with both teams, let alone be in this region at all if this wasn't as big of an emergency as it is. So we need both teams to work together just this once! We need fire support in a large-scale battle in the near future."

Shelly looked annoyed with the two. "Why should we? What do we get out of this?"

Tobias answered her with one word. "Survival!"

Gary explained. "I'm sure you've all heard of the Shadow Empire. Well apparently, they're back from the dead, figuratively speaking, and their weakest members are each evenly matched with Tobias here, who is the 3rd strongest member in the A Class at the Crimson Academy. Meaning he is the 4th strongest person in the entire academy. We seriously need all of your help.

Tabitha spoke up. "No way! There's no way I'm working with him!" pointing at Matt. But Archie and Maxie had different plans. They talked for a bit and came to an agreement. Maxie spoke up.

"We've heard of the Empire. They were powerful a century ago. It took the combined effort of all the regions to supposively wipe them out, but it looks like the history books were wrong. We will help y-"

He was cut off by the sounds of screams and explosions.

 _Oh god!_ Thought Tobias. _They found us!_


	17. Chapter 15 Old Enemies pt 4 (Hoenn 2)

The 4 Admins, Archie, Maxie, Gary, and Tobias rushed out to see a slaughterhouse. The Empire had found them and planned to wipe out both teams at once. Gary and Tobias did exactly what the Empire wanted them to do. Lead both teams into one spot and wipe out everyone in that cave without mercy. Maxie spoke up. "Take the Admins out of here. Save as many of both teams as you can. Run as far away from here as possible. When you're finally safe, head to Sky Pillar, I have an old friend there. She'll join you and get you all back to your academy."

Shelly spoke up. "But what about you two?"

Archie responded in a stern tone. "We'll stay behind. Draw their fire away from you."

Shelly went into shock, but Courtney shook her out instantly. "Come on. We've got to go!" And with that, Maxie and Archie, as well as their mega-evolved pokemon, were attacking the Empire's members getting their attention. The 6 snuck around them and picked up any Aqua or Magma member that was still alive, or just holding on. There weren't many survivors. They picked up 20 more people when they saw the Empire closing in on them. Shelly and Courtney were almost in tears. Their leaders, the people they looked up to, were dead. Tobias quickly turned around and faced the oncoming squad. "Leave me! I can hold them off! All of you, get to safety! I'll try and catch up soon!"

And with that he sent out four of his six pokemon out at once. "Darkrai! Latios! Heatran! Genesect! Come out now!"

The four burst out and immediately fired at the field squad in front of them. The opposing pokemon did the same. The attacks collided and there was a huge explosion, collapsing the cave, with Tobias and the Empire field squad in it.


	18. Chapter 16 Old Enemies pt 5 (Hoenn 3)

Gary and the others managed to escape, but many were caught in the explosion, including all but 5 grunts, the Admins, and Gary. They all looked over the rubble and began to mourn the dead. Gary was almost bursting into tears. Tobias was risked his life for them. They got up to travel to Sky Pillar when Matt heard a the sound of rocks being moved behind him. He and Gary looked back. Had some of the Empire squad survived? Gary's Electivire was sent out ready to attack.

A figure climbed his way out from the rubble. He was covered in blood and his clothes were torn in several places. "Looks like God is with me today!" he said and collapsed. It was Tobias. He survived.

Matt picked up Tobias. "Sounds like the kid is still alive. So that's good." He then proceeded to look at Tobias's belt, where his team resided. "Jesus! This guy is achieving the near impossible over here. It seems like all 6 pokemon are accounted for. He must have brought them back once the explosion began."

Gary was relieved. "Good. Matt, I need you to carry him to Sky Pillar. It's a miracle he's alive now I don't think he has the ability to walk. Now come on. Let's get to Sky Pillar."

The travel was long. Tobias still was not getting up, but at least he was still alive. After climbing up to the top, the 11 people came face to face with a woman. She looked at all of them with suspicion.

"I saw the explosion from Lilycove Cave. Would any of you care to explain what happened?"

Courtney spoke first. "Zinnia, please. We can discuss this later. Right now, we need your help. The kid here will explain."

Zinnia looked at Gary. He took a deep breath and spoke. "Hello. I am Gary and that over there is Tobias. His condition is the result of the explosion. I'm sure you've heard of the Shadow Empire?" She nodded. Gary continued. "Splendid. Saves me the trouble of explaining it to you. Tobias and I set up a meeting with Aqua and Magma to convince them to help us fight the Empire. However, things went south very quickly. The Empire attacked us and wiped out both teams, including the leaders. We're all that's left. Tobias caused the explosion in order to cause the cave in to prevent a field squad from attacking us. We need your help getting back to Kalos.

"No one is going anywhere!" A S.E. member stood behind them. He was another survivor of the explosion. He looked at Tobias, still unconscious. "The main threat is still down. I'll wipe you out here and now."

Suddenly, Tobias got up and hobbled in front of the group. "I wiped an entire squad. What's one more?" he said faintly. But before he can do anything, he collapsed. Zinnia caught him and sent out her Salamence, which instantly mega evolved.

"I've heard a lot about you people." She said coldly. "People like you deserve to not exist." Before the Empire soldier could do anything, he was engulfed in an amped up hyper beam, and instantly disappeared out of existence. She looked at Tobias. _Damn._ She thought to herself. _This kid's will to live is insane. Not only that, his pokemon's energy is crazy. I'm impressed. He clearly has guts_. She looked up at the others. "Everyone get on my pokemon. We will be in Kalos in an hour. Looks like you all need my help."

All 12 people got onto her Salamence and took off. They got to Kalos in record time. As soon as they got to the academy, they saw Saturn and Red in the Hospital Room, along with 8-20 members from each team recovering. The five Aqua/Magma grunts layed down on the beds to recover, while Tobias was taken off to the Emergency Room due to his critical condition. Zinnia followed. As for the Admins, they left to the Mess Hall to get a well needed meal.

Gary walked over to Red. "Same scenario as us?" asked Gary.

Red nodded.

"Where's Paul?"

"He is in his room resting. He has a broken arm, and once it was put into a sling, he left. As far as I know, Dawn is still with him." answered Red.

Saturn chimed in. "Galactic was destroyed when we got there. We set up a meeting to those who still followed Galactic. But when we got to the meeting point, everyone was dead, except one. Mars and Jupiter are with him now."

"Who is he?" asked Gary.

"You'll see soon enough."

Gary looked up. _Seems like everyone here has had a rough week or two. I know it has been for me. Still, you'd think Green and Silver would be back by now. Hopefully they're being extra precautious. I hope Rocket is a better success than everyone else was._

At that point Green called all of them at once. " _This is Green. Rocket has entered! Is anyone there? Hello? Anyone?"_


	19. Chapter 17 The Truth

Silver and Green, along with intervals of Rocket members, showed up to the academy in a few hours after Green heard from Red. While Red, Silver, and Giovanni explained to Cynthia the situation, Blue took Green to a private room. When she concluded that they were alone, she spoke.

"I have the feeling you haven't told me the truth about you and your past. I would like to know the full story."

Green looked at her with an annoyed expression. "I honestly don't think that this is the right time for that."

"Start talking! We have time."

Green sighed. "If you wish." He then proceeded to tell her everything. He began with his father, how he was the 75th trainer under Emerald, but like most, abandoned half way through because he couldn't handle the intensity of it. After leaving Emerald, he went back to Kanto where he settled down. Within 10 years, he got married and had a son. 5 years later, tragedy struck. A Field Admin from the Empire along with 5 more people, one of which they met in the graveyard, were sent to extract the information of Emerald's location from him. He refused, and he along with his wife were killed. All that was left was Green, who was a toddler at that time. The Empire assumed that he would die in the flames, and left him be, proceeding to set the house on fire.

"Thankfully, Oak was there to save me." Green said. "That memory, the fact that I was too weak to help those I cared about, haunt me to this day."

Blue was shocked. She thanked Green for the truth and left the room. She stopped and tried to go in the direction Green was going to ask him one last thing, but when she turned around, he was gone.


	20. Chapter 18 Emerald

Green teleported away to his Master's secret island. Every time he visits, he is still awestruck by the island as a whole. The island has insane weather patterns, allowing for different seasons, climates, and geological structures everywhere. Around him were pokemon, his pokemon. Training day after day just has Green has done before. He entered a nearby cave and spotted his Master sitting at a table. Without looking up, Emerald spoke. "Welcome back Green. I made tea. Have some."

Green studied the table. Two cups. Both were steaming. His Master knew he was coming. "Two cups" Green pointed out. "This means you also know why I am here."

"Indeed I do"

"Then give me the answers I need"

The Master looked at him. "You want revenge. I can see it in you. You say you are doing this to save everyone, but in reality, you're doing this for yourself. I can see your plan. It won't work. Do you really think that sacrificing your friends-"

"Allies" interrupted Green.

"FRIENDS is the way to go?" Emerald continued. "You will fail. You're friends will then fight against you."

"May you please explain."

"The Fallen One has the ability to take control of whoever the Empire beats. All of those Rocket Grunts, Aqua, Magma, Plasma, and Galactic, are now under the rule of the Empire and the 8th Master. Yes. Even your own father!

Green went into shock. His father? Now another member of the Empire? His Master went on. "Last time I checked, he has taken the place of the Field Admin that killed him so many years ago. What's more, all memories from their previous lives are erased. But there have been few throughout history who seem to be an exception. For instance, 120 years ago, a Squad Leader jeopardized an entire mission just to try and beat a man who was his rival in his previous life. Another scenario was when a member defected during the Great Veilstone City Fire, after witnessing the death of an eevee, which sparked a memory of the fate of his Espeon in his previous life."

Green was furious with the Empire and the 8th Master. "I need your help. Please fight with us."

"Green. You know the rules." Emerald said sternly. "However you have an ally just as strong as you. Head back to the academy. You will find this person currently helping someone from your Class."

And with that, Green teleported back to Kalos.


	21. Chapter 19 Midnight Father

Green teleported back to the academy and looked out the window. "It has been a long week for all of us." He said to himself. "I need some rest. I'll search for the other apprentice tomorrow." With that, he returned to his dorm room and fell right asleep.

Around midnight, he began dreaming. He was alone. A white void surrounded him. Looking around, he began to hear footsteps. However, there was no one there. Then, like magic, a man appeared out of nowhere. Green began to tear up. "Dad?" he cried. No. This isn't real. His father is now his enemy. But there he was, right there in front of Green.

Then, shadows engulfed his father. When the shadows cleared, Lunick was different. His black Empire suit. This was his father now. Green tried to punch him, but a mysterious force prevented him. His father laughed. "March 3rd. See you then." Green then woke up.

Green shook Red awake. "Green? What is it?" Red wearily asked? He checked the time. "What's up? It's 2 am."

Green said nothing. He then called Blue, who surprisingly was still up. "Wake up all Class A girls and meet us in our rec room quickly!" Green said. Blue did what Green asked.

While Blue woke the girls, Green went to wake up the Class B team, as well as the reinforcements. This left Red to wake up the boys from Class A.

Within an hour, all of Class A, the B team, Hoenn admins, and Rocket's Executive board were present. Everyone looked at Green. He said two words, but everyone understood what it meant: May Third.

The next day, Green, Red, Gary, and Tobias discussed their plan of action. "We train everyday. We will all go through the same training regimen as I did when I trained with Emerald." said Green. Everyone agreed with this.

Later on that day, Green was walking alone in the halls when a girl bumped into him.

"Oh sorry" she said. "You ok?"

"Yeah"

"That's good. Hey, I'm looking for Tobias, you've seen him?

"Try the Battle Room"

"Thanks!" she yelled and ran off.

Green paused for a moment and smiled. He then followed her.


	22. Chapter 20 The Second Apprentice

Green followed the girl all the way to the Battle Room. She put her bag down behind the stands and began to train with Tobias, giving him pointers about certain battle situations, as well as teaching him how to mega evolve his Latios, as well as how to use it. While all of that was going on, Green snuck a note into the girl's bag. The note read: " _11 pm. Courtyard."_

That night, Green was waiting on a bench when the girl walked up. "You again?" she said. "What do you want?"

"Please Zinnia. Don't tell me you forgot about me." said Green.

"Well Green. How long has it been?" asked Zinnia.

"Too long. Fancy seeing you here."

"I showed up with Tobias and Gary. They were in terr-"

"I know who you are" interrupted Green. "You are the apprentice to N. One of the remaining Master-Elites".

Zinnia tried to play dumb. "What? I don't know what your talking about."

Green saw through this. "Your Master contacted my Master, Emerald, a while ago. Tomorrow, meet me in the Battle Room. I want to test your strength." With that he left.


	23. Chapter 21 Battle

Zinnia showed up to the Battle Room the next afternoon. Green and Red were already there. Red had agreed to be the ref for the battle. "This will be a 1v1 battle!" he cried. "Once a pokemon is sent out, that's it! After 20 minutes, if no pokemon has fainted, we end in a tie!

Green and Zinnia sent out their pokemon. Green sent out Charizard and Zinnia sent out Salamence. Both immediately mega evolved, and a spectacular battle unfolded. Both sides kept attacking, but no one could gain the upper hand. Attacks landed, but none of their pokemon seemed to want to budge. They just kept going. Mega Charizard countered his opponent so perfectly, but so did Mega Salamence.

The battle attracted more and more people. The spectators were cheering, but none were more excited than the two battling. It's been so long since they've fought someone as strong as them. Blue, from the stands, noticed something change in Green in that battle. For the first time, he seemed to have fun in a battle. To her, Green looked like a trainer in his first battle, determined to make a good first impression. She smiled. She couldn't believe she had -.

Her thoughts were interrupted by Red.

"10 minutes left!"

Tobias was awestruck. Green has found his match. He looked at Zinnia. This person was a force to be reckoned with.

Green ordered his Charizard to stay on the attack, and Zinnia ordered her Salamence to do the same.

Meanwhile, Red noticed something odd. Both people seemed to be holding back something, but couldn't figure out what it was.

"Charizard! Blast Burn!"

"Salamence! Hyper Beam!"

The attacks collided making a huge explosion. When the smoke cleared, both pokemon were still standing. The explosion did little damage to them. Gary was shocked. That explosion was stronger and larger than the one Tobias caused in Hoenn, yet both trainers, as well as their pokemon, were perfectly fine. "Thank god for the barrier protecting the stands" he said to himself.

"Time!" Red shouted. Both trainers returned their pokemon. They shook hands, and left the room, leaving the awestruck spectators to their thoughts.


	24. Chapter 22 The Weeks That Followed

The talk of the Academy during the next few weeks was the battle between Zinnia and Green. Theories were everywhere. One trainer believed that Green took it easy on her. Another one believed that Zinnia was stronger. But only Class A, as well as the B team knew the truth. The two were evenly matched. No trainer would be able to ever beat the other.

The training that the Class A, B team, and the reinforcements received from Green, and now Zinnia as well, were cruel and could be considered inhumane. Many wanted to quit, but they stopped themselves because they knew they had a job to do. Throughout his many dreams relating to the Empire, he learned more about them, how they came to be, why they decided to fake their demise, and how they have gotten stronger over the years.

Green and Zinnia decided to let the team take a break during the Christmas season. Blue and Green traveled Kalos together. Red and Yellow went back to Kanto. Gary, Crystal, Tobias, and Zinnia traveled to Sinnoh, where they split up. Gary and Chrystal explored the Solaceon Ruins while Tobias and Zinnia traveled to the three lakes. The rest of Class A either traveled on their own, or found someone to go with. Paul and Dawn decided to explore Unova. Many members from Class B decided to stay behind at the academy.

Each group had their own adventure during the break, each with a story to tell. Sapphire managed to convince Ruby to go with her back to Hoenn. While there, they visited their parents and explored the region, remembering their adventures there. They decided to skip Lilycove, as it was still recovering from the Empire attack from a while ago. They met up with Wally there as well, and after being with them for a day, left the two and traveled on his own. Sapphire and Ruby had a date in Mauville city and then Ruby entered in the Region-wide Christmas Contest, while Sapphire watched from the stands.

As for Red and Yellow, Kanto was an adventure of its own. Red and Yellow reminisced in their adventures in Kanto, and camped out in Viridian Forest. There, the two sang campfire songs and told ghost stories. Tobias and Zinnia had fun exploring the three lakes. Everyday the two traveled together, the connection between the two grew tighter, but neither of them knew what to say to the other. Gary was a different story. One winter evening, he and Crystal were together having dinner.

"Kris," Gary stated. "We both have so much in common. We both are out for knowledge, and well as new pokemon. I have great feelings for you. Will you-"

"Yes" Interrupted Crystal. "I have feelings for you too. I'll be your girlfriend." The two then celebrated.


	25. Chapter 23 Green and Blue

Green and Blue left the academy 3 days before Christmas Eve. Green was originally planning to spend his break alone in Kanto, but Blue convinced him to travel with her throughout Kalos. Both had different agendas while they were there. Blue wanted to visit Parfum Palace before anything else, while Green wanted to visit the Chamber of Emptiness. After much debate, they compromised with going to the Palace first, as it was on the was to the Chamber.

When the two got to the Palace, Blue was like a little kid, getting distracted and mesmerized by everything. Green was the opposite. The palace was too fancy for his taste. The Chamber was a different story for both of them. Green was in awe by the mystery behind the fact that nothing could live there.

"In a way, it's quite peaceful." said Green.

"You're crazy! This place gives me the creeps." Blue then walked out.

Green stayed for a bit longer, taking in the silence, then followed. The two then decided to try and find the Pokemon Village. Green allowed Blue to take the lead. However, she only led them in circles and managed to get them lost, so it was up to Green to get them out.

They spent the next day touring the Pokeball Factory and then visited Anistar City, more specifically, the city's sundial. Blue was constantly in awe at everything, while Green showed some interest.

The two decided to spend Christmas in Lumiose City. In the beginning, they split up and did their own thing. Blue rushed from café to café, while Green checked out the Stone Emporium and the art museum. They bumped into each other hours later in a random café.

"Green! Great to see you!" Blue said. She sat down next to Green and she ordered her lunch. She noticed a few bags next to him. "What do you have there?"

Green quickly covered them up. "Nothing important."

"... If you say so." Blue looked at him with suspicion. "Anyways, I want to check out Boutique Couture for a while. What to come after we eat?

"Sure. Why not." The two got their food and began to eat. Once they finished, they left and walked to Boutique Couture. When they got there, Blue let out a barely audible squeal. She rushed through the aisles picking out dresses and went to try them on. Green on the other hand, had his eyes on a pair of sunglasses.

Green waited outside the dressing rooms for Blue, checking himself in the mirror with the sunglasses while he waited. Blue walked out wearing an extremely over-the-top dress. "Hey babe, what's your opinion on this?"

She immediately realized what she said and her face turned bright red, hoping Green didn't hear. But he did. His face turned to a shade of pink. He didn't know what to say.

After a minute of awkward silence, Green spoke up. "The dress is a bit much, don't you think?"

Blue came to her senses after that and rushed back to the dressing room to try on a new one, as well as to figure out what just happened. She looked at herself in the mirror. She shook her head. The two were only friends, right? But looking back on that moment, she noticed that for a split second, Green had a flirtatious grin. Blue turned bright red again. She quickly calmed herself down and came out wearing a beautiful cobalt-colored dress.

Green studied it. It was fancy, but not over-the-top. The color really shone on her. And the design on the dress was something else. He nodded in approval. "I think it looks interesting to say the least."

Blue happily changed back to her normal clothing and was about to buy the dress when she noticed the price tag.

"Jesus! $156,000?!" Blue sadly put the dress back and began to walk outside. Green stayed behind for a while looking at the sunglasses once more, and soon walked out with a bag.


	26. Chapter 24 Christmas

That evening, the two made their way up to Lumiose Tower. When they got to the top, it began to snow. The two stood quietly, leaning over the edge. After a while Blue broke the silence.

"Hey, about what happened earlier today…" Green looked at her. His face was pink, but Blue couldn't tell if that was from the cold, or if he was actually blushing. She continued "I hope that didn't make you feel too uncomfortable in any way."

"No. Not really. Just wasn't expecting something that sudden."

Blue sighed in relief. Green just laughed. "Why? Did you feel uncomfortable?"

"Extremely. It just sort of, came out"

Green laughed some more. "Just tells you about the two of us. Doesn't it?"

Blue's heart began to pound. " _Did… did he just flirt with me?"_ She thought. "I… you… I mean…" she stumbled, her face turning redder by the second. Green just laughed.

The two stayed up there for a few hours talking about everything. Blue tried to flirt with Green, but was too embarrassed to do so. Around midnight, they went back to their hotel room. There, they chatted with Red and Yellow, who were spending their Christmas in Pallet Town.

The room finally went quiet, as the two fell asleep. Well, only Green did. Blue was trying to find a way to make a move on Green, and around 3 a.m., she had an idea.

The next morning, they gave each other their present for them. Green insisted that Blue opened hers first.

The first thing she saw was a sparkling stone. "Is this… a mega stone?" She asked.

"Yep. A Blastoisite. I'll teach you how to use it sometime this week."

She continued on. Other items included a new hat a note that read " _In the closet"_. She opened the closet door and saw a bag hanging in front of her. She picked it up and brought it back to Green, who now had a giant grin on his face.

Opening the bag, there was another bag, as well as a small clothed box. Opening the box, she found herself staring at a gold necklace. She was awed by its beauty. The gem was a diamond with a center of emerald. She immediately put it on.

She then opened the second bag and almost collapsed. It was the dress she liked yesterday. Green had bought it for her. (No. He did not buy the glasses as well).

She charged at Green and tackled him. Almost hugging the life out of him.

Green was next. His first gift was a new bag. This one was more durable that his current one, which was starting to wear out. His next gift was a pair of gloves, similar to the ones that red had, but was made out of more durable material.

He was going to hug Blue and a thank you, but before he could do so, she handed him a slip of paper. " _Look up_ ". He looked up and saw a mistletoe in between the two of them.

Before Green could do anything, Blue made her move. Her heart pounded with excitement. Her Christmas wish had come true.

As for Green, his was first very surprised about what was happening, but he soon accepted that. He was happy. It was the first time he saw anyone as something more than a friend, ally, or a stranger.

As the two were spending Christmas together, someone watched from outside. Despite being hooded and obviously out of place, the people around the figure didn't seem to notice the person. The figure just looked at the two, and grinned.


	27. Chapter 25 Strange Figure

Christmas break had come and gone. And now everyone was back to training. Zinnia worked with battling, while Green focused on Mega Evolution with those who haven't mastered it, including Red, Tobias, Blue, Sapphire, and Wally. Green and Zinnia found training battling each other. They pushed each other to their limits and beyond. Again, the same hooded figure watched the training ensue from the woods close by. As before, no one seemed to notice him. Green looked towards the woods. He thought he saw something, or someone, standing there, but he saw no one. He dismissed it as his imagination and went back to training. When he turned away, the hooded figure emerged from the shadows to watch once again.

As the hooded man began to leave, he heard a stick snap nearby. Turning around, he saw a second figure. The second figure ran, while the first chased after.

The second one soon blocked by a cliff on one side, and the first figure on the other. The first man then spoke. "You can see me despite the psychic energy around me. Despite your encounter with the Empire all those years ago, you're still you in some ways." He took his hood down. It was Emerald. He had been keeping an eye on his apprentice and his progress.

The second figure spoke. "Ah. It's you. I did not recognize you. You have gotten wiser and stronger in the years, but not me. I've grown weaker in some ways. Though my strength had stayed the same, I can no longer detect another apprentice or elite's energy." He took his hood off. A giant scar ran down his left eye. His hair was gray, but still had a touch of black in some areas. He continued. "I've hidden my energy in my old age. I can no longer be detected."

Emerald spoke. "You are here to see the boy, aren't you?"

"To watch him, to be more specific. I trust you have told him what I told you."

"Indeed I have"

"And the Empire's plan?"

"Told him through a dream"

"Good." Said the man. He then looked at Emerald. "How is he doing?"

Emerald looked at the man. "You should be the one to see for yourself. Meet me here tomorrow at dawn and you shall see." The two men then put their hoods up and left.


	28. Chapter 26 From Another's Point of View

It was still dark out when the man showed up to the cliff. Emerald, in a black cloak, was waiting for him.

Emerald looked at the man. "Shall we begin?"

The man nodded. The two walked over to the edge of the words. There, they saw Green meditating. The man spoke to Emerald. "How is it that he isn't detecting your energy?"

"You are not the only one who can hide it."

While Green went along with his daily life, the stranger watched from the side. He saw Green train all of his friends for the upcoming battle. The stranger smiled. "You've taught the kid well".

He watched Green train for a while. And then turned to leave when Emerald grabbed his shoulder.

"He needs to know the truth" the elite said.

"He cannot know. Not yet. If he's anything like me, he'll come search for me. He needs to be here, surrounded by people he cares about. Not be out and about, searching for some old man. With that, the stranger left. Emerald teleported away.


	29. Chapter 27 The Island

Time was growing short. They only had a 6 weeks left before the attack, and Green knew how to spend it. Long, long ago, the apprentices of Elites had to spend a month on a large island. There, they would complete different challenges set up by the Elites. Green took the team there. When they got to the island, he explained what they were going to do.

"You will spend a month on this island." He said. "Each day, there will be a new set of challenges for you all to face. These challenges will be set up by Zinnia and I. These challenges are not going to be easy, and some can be dangerous. In order to make you all go beyond your limits, those who don't complete a challenge don't eat for 3 meals."

Many looked at Green with disbelief. Some wanted to go home. Only a few accepted this with enthusiasm.

Green looked at the group. "We shall start off easy. You will have 6 hours to build a shelter large enough to fit all of us. If you don't finish it in time, we all sleep outside for the month. Oh. And before I forget, you will be doing this is pouring rain."

With that, he sent out his Golduck. His Pokemon used Rain Dance and a heavy downpour started. "Your time starts now!" He yelled. And Class A and the B team were off to work. (Sadly, they didn't complete it in time. No one could agree on what do do).

Everyone trained hard for the next month. During that time, they were taught how to work together, unique strategies, as well as ways to amp up attacks. By the time the month was over, everyone was at their peak. Green felt that they were ready. They traveled back to the Academy where Green gave them their last order for a while. "Rest up." He said. "You can relax, but don't stop training. With that, they left. The days leading up to the attack were calm, but a week before the attack, things changed.

Green was in his dorm room when a voice went through his head to head home at dusk. At first he was very confused. He didn't know this voice. Also, what "home" did he speak of? Green spent that day wondering what "home" meant. Around noon, he had an idea. That night, he teleported Pallet Town.


	30. Chapter 28 The Meeting pt 1

Green teleported to his old, burnt down house. He walked around it. It was still standing, but at the current state, it was barely livable. He walked around his house, on guard and ready for a surprise attack. He entered his old room and saw a piece of paper on a table in there. It was a poorly drawn picture of a Charmander. Green drew it the day his life changed. He was going to show his parents it, but-

Green stopped the memory there. He didn't want to live through the pain again. He picked up the drawing and was about to put it in his pocket when he noticed some writing on the back. Green looked confused. The writing was new. Green read it. "Great picture for someone at that age." it read. "Head to Viridian Forest. It's time we speak again."

Green got tense. Someone had been here recently and wants to see him again. This means that whoever it is, they had spoke to Green before. Tick crawled into his pocket and Green was off, ready to meet the person. Green reached the forest and traveled into it. The night sky made the trees seem like they were alive. Green looked around, he could not see anyone yet. He wandered aimlessly for an hour or two before he reached a clearing. The ground beneath him turned to stone. He noticed a hooded figure standing in the middle. When Green got close, the figure spoke. "Nice to see you again Green." the figure spoke. "Or should I say, _my son_!"


	31. Chapter 29 The Meeting pt 2

Without a second thought, Green sent out his Charizard and chaos started. Charizard was on the attack, constantly blasting at Green's father. His father, expecting this, dodged all the attacks. Green was guided by pure rage, ordering Charizard to attack with full force.

Suddenly, his father sent out a pokemon, a Swampert, who immediately mega evolved. Charizard did the same. The battle ensued.

"Charizard! Blast Burn! Full power!"

"Swampert! Hydro Cannon!"

The attacks collided resulting in a giant steam explosion. Charizard bursted through the steam using 'Shadow Claw' and landed a direct hit on Mega Swampert, which immediately retaliated using 'Hydro Pump', landing a direct hit on Charizard. Both attacks did little to each other. Charizard then came at Swampert from all directions with his speed, using 'Shadow Claw' for every hit. Then Charizard dived from above and delivered a 'Dragon Tail' directly on Swampert. Throughout all that, Swampert stayed standing.

Swampert was not as fast or as strong as Charizard, but did surpass Charizard in Defense and Endurance. Swampert used 'Hydro Cannon' at the ground, which dug through the earth. The attack came up again at random locations on the battlefield, hitting Charizard multiple times.

Then his father was hit with a large jolt of electricity and fell to the ground. Tick had crawlen to Green's father and attacked. Swampert turned around for a split second. That was all Charizard needed. With a devastating blow, Charizard KOed Swampert.

Green returned Charizard and walked over to his father. Tick sat on his father's neck ready for Green to give the order. "Normally I'd give you time to get out of here. But in this case, there's no chance I'm letting you go."

Before Green could give the order, he detected a small out of energy coming from his father. Green hesitated. If this man was with the empire, his energy should be much darker. Green ordered Tick off of his father and his father stood up, his hood falling in the process. Green had a clear view of his father. He had a giant scar which ran down his left eye. His hair was gray, but still had a touch of black in some areas.

His father spoke. "It's time you knew the truth." He put his hood back up. "I am not with the Empire. I asked our master to lie to you so you won't go after me." He then turned to his Swampert, returning it to its pokeball. "Looks like you have been taught well."

Green had many questions. "Why? After all of this time, why now?"

His father did not answer.

"Why did you want to see me?"

"So I can join my son in the battle against those who killed my wife, your mother." His father looked at the rising sun. "Come. It's time to discuss what to do." With that, the two teleported back to the Academy.


	32. Chapter 30 Before Dawn

_March 3rd 5:30am_

 _Green woke us up around 4:00 am. He wants everyone outside before 6:00 to be ready. Everyone is on edge. Everyone is scared. They may be hiding it, but it's true. None of us have ever fought in a life-or-death battle (Except for about 5 of us). I worry for everyone. We've all wanted to say goodbye to each other last night, in case anyone dies, but Green wouldn't have it. He said he wouldn't let any of us die. That gave us some hope. Well, it's time to go save the world._

Sapphire closed her diary and took a deep breath. "This is it." she said to herself. "I can stay in here and be safe, or I can go out there and fight with everyone". She looked outside and saw Ruby standing out there. Sapphire hated herself for convincing her boyfriend to join them. She cursed and grabbed her stuff, joining the others who were going out to join Green and the others.

Out of everyone out there, Red seemed the most pumped. He had one-on-one training with Green's father for the past week. He was ready. He ran up to Lunick and greeted him. Green's father had become his new role model.

Soon everyone had shown up and were standing in front of Geovanni, Zinnia, Lunick, and Green.

Lunick spoke first. "Today is the day the strong are separated from the weak. You will all be pushed to your limits and beyond. Every battle you've had, every second you train, every test you took has been leading up to this point. But remember, this is not just an ordinary battle. You will be fighting for the lives of your own, your loved ones, and everyone else. The Empire is not something to be taken lightly! They will attack without mercy and would rather die than surrender!"

Green stepped forward. "Remember, the Empire is strong. If you lose, you run! If you are caught, there is a 90% chance you will die and then there is another 60% chance you will be revived and join their ranks. If you lose or close to losing, call of backup immediately. We'll have any spare Rocket members defend you as someone heals your Pokémon."

Zinnia spoke last. "In order to minimize the amount of casualties, the entire academy was cleared yesterday. But still, try not to destroy the buildings."

When the three finished talking, everyone ran to a different location and waited. There were people everywhere, along with hundreds of members from Team Rocket and the remnants from the other teams hidden in bushes, trees, and in buildings. From their hiding places, they watched the sun start to rise.


	33. Chapter 31 The Empire Strikes (Back)

(Sun's POV)

"Daytime. Finally." he said to himself. He looked upon the rising sun and felt conflicted. His body wanted to relax, just for a moment, but his mind had other plans. He knew that relaxation, even for a second, could be dangerous. The Empire could attack at any moment. He looked around, hearing the sounds of the birds and wind around him. He closed his eyes for a second. In that second, everything changed.

Red's (POV)

The sky darkened. The mild breeze stopped, bring in cold wind. The time was upon them. Red looked towards the sun, only to see waves upon waves of figures heading towards them.

"INCOMING!" someone shouted, and Green and his father ran out, sending out their Pokémon. There was no turning back now.


	34. Chapter 32 The Beginning of Chaos

The war had begun. The Empire's forces began to cover the sky, only to dive down and begin attacking anyone they saw. Sapphire and Ruby tag teamed anyone they saw, but were being easily pushed back. A hyper beam was shot at Sapphire herself and she saw her life flash before her eyes. The beam hit the ground and they was a giant explosion.

"SAPPHIRE!" Ruby cried, with tears running down his face. However, when the smoke cleared, Sapphire was still completely fine. In front of her was a Latios.

"What part of be careful don't you two morons understand?" The Latios returned to Tobias. "Next time it won't be as simple." Tobias turned his attention back to the group he was fighting. In a swift move, his Darkrai engulfed the group in a sphere of nightmares, putting them in a nightmare-induced coma and rendering his opponents useless to battle.

Sapphire joined back with a now enraged Ruby. He was holding his opponents off when Sapphire came in to help deal the finishing blow.

Meanwhile, Gold and Silver had to team up with Black and White to deal with the opposing forces. Black and White were almost done for when Gold and Silver jumped in. They managed to drive the enemy forces back for a few minutes.

But things weren't going to well for some other people. The Empire managed to make their way into the Mess Hall, with Iris, Wally, Sun and Moon chasing after them. Wally was the first to go.

As soon as the heroes entered the Mess Hall, a Thunder attack headed straight towards them. They all dove out of the way, except for Wally who was too slow to react. Iris watched as he took the Thunder attack and flew backwards. His corpse lied there, burned and barely recognizable.

"One down. Three more to go." One of the Empire Grunts laughed.

This threw Sun and Moon into a fit of rage as they charged at the enemy.

"NO WAIT!" Iris cried, but it was too late. Sun sent out Decidueye and Moon sent out Primarina. The Pokémon charged at the Empire only to be shot down. Sun and Moon followed soon after.

"And only one remains!" The grunt laughed. "We'll be fair and give you a moment to pray".

Iris looked at the men about to attack her and one of them looked very familiar. The hood made it difficult to be certain, but Iris noticed that one of of them had long green hair, as well as a red eye patch staring right at her. "Ghetsis?" She cried out. "Is that you?"

The man gave her a sinister grin and sent out a Hydreigon. The pokemon used Dragon Pulse and Iris closed her eyes. From outside, a giant explosion could be heard.


	35. Chapter 33 From One to Another

Iris opened her eyes. She wasn't dead. A man stood in front of her. He had blue hair and a stern face. The figure who just attacked spoke. "Leave. This one is mine."

The other Shadow grunts nodded and took off. And the other man spoke to Iris. "Run along now. You don't want to get caught up in this."

When Iris was gone, the hooded figure spoke. "Well, well, well. It's good to see you again. When was the last time we spoke? God. It must have been two, maybe three years ago. Where have you been?"

"In solitude. Honing my skills so I can one day return and continue where I left off. But now I see that can no longer happen.

"My offer still stands. Cyrus, you know we can always use people like you."

"Oh Ghetsis, my answer is still no. Why would I ever be a pawn in someone else's game?"

"But Cyrus, from one leader to another, I beg you to reconsider. You're missing out on so much. The power. The advancements. The thrill." Ghetsis said with a sinister grin on his face. "But if that is your final answer, then I guess I'll just eradicate you! His Hydreigon fired a Dragon Pulse at Cyrus and the battle began.

Cyrus sent out his Gyarados to block the attack and used Ice fang on Hydreigon. The attack crippled the opposing Pokémon, rendering it useless. Ghetsis sent out Eelektross, and in a single attack, Gyarados was wiped out.

Ghetsis spoke up. "This is going to be interesting".

Meanwhile, the bulk of the Imperial forces were attacking Green, Lunick, and Zinnia. Empire forces were getting wiped out by each of them.

Suddenly, a large, black glider flew by Green and felt a dark energy. Green chased after the glider. Green got a good look at what he was up against. He saw a woman on top of the glider. Without thinking, Green ordered Charizard to fire at it. The attack did nothing. The person had sent out a Braviary which had used "Protect".

Green was in shock. No one ever had blocked any of his attacks and came out unscathed, even with using 'Protect'. This new person had to be an Elite Trainee. "Well, well, well" the woman spoke. "If it isn't the famous Green. Apprentice to Emerald. Sorry kid, but I got more important things to do as of right now."

"You're not going anywhere!" Green shouted, rushing after the glider. "I'm taking you down here and now!"

"Just try to Greenie!" The woman said as she flew off, with Green chasing after her, closing in fast.


	36. Chapter 34 Taken

The woman landed her glider, allowing Green to land. He looked around, they were around 5 miles from the academy. He was too far away to help anyone, but that didn't matter. His priority was the Empire. The others didn't matter.

That thought stopped Green dead in his tracks. Oh God! He thought. What have I done?

The woman smiled. "Oh this was just too easy. I know I can't defeat you, and you won't go willingly… not without reason."

"What do you mean?!" Green shouted.

"See you soon Greenie!" said the woman as she was teleported away. Green sent out his Alakazam and teleported back to the academy. When he got there, it was quiet. The scars of the war were there, but not a soul could be found.

"Hello?" Green shouted. He got no response. Oh God. They've been taken! Green said to himself. Green fell onto his knees. His Master was right.


	37. Chapter 35 Mt Silver

Green wanted to cry. To yell. To do something. But he couldn't. Something was holding him back. He slammed his fist on the ground. "DAMIT!" He cried. "There's no one left!"

"Well, that's not entirely true."

Green heard footsteps as well as the sound of a body being dragged across the Earth. Green didn't even care who it was.

"You know, most people look when they're being spoken to"

Green turned around. It was Cyrus and an unconscious Ghetsis. Cyrus spoke again. "You know neph- Green, your father told me just the other day how you seemed very capable, and ready for anything. I don't see that here." He gave Green a stern look. "All I see is a child in an adult's body. You're arrogant, cold, and rush into things without thinking. That's why you lost today. You got cocky and set your own goals ahead of your own friend's lives."

He handed Green a map. "This'll get you to the Imperial Capital. You're on your own here. It's time you figure out what to do on your own. I'm not risking my life while you're still like this."

Green looked at him. "Is that all?"

"Before you decide to foolishly kill all of your friends at the Capital, head to Mt. Silver. There's a friend waiting for you there. Oh. And you won't find her if you teleport. I suggest you fly." And with that he left, with Ghetsis being dragged behind him.

Green sent out his Pidgeot, which mega evolved and Green hopped on. "To Mt. Silver!" And he was off.

Along the way he began to think. Who was waiting for him? Why Mt. Silver? And most importantly, where to start looking?

Green landed at the base. I'll start here. It was freezing. Green was stupid enough to not bring a jacket. Cyrus was right. He was over ambitious. Green started to hike up the mountain. As he got colder and colder, he began to notice his surroundings, for the first time in forever. It was so peaceful. Such peace. So quiet. Green could hear everything. He could hear the crunching of the snow beneath the Pokémons' feet.

But then things took a turn for a worse. A snowstorm hit and he was in the middle of it. Green tried to run, but the storm seemed to follow him. Green started to get heavy. The world around him started to spin. Green tried to keep going, but after a few more steps, he fell into the snow. Green blacked out.


End file.
